Genetic Switch Systems Research Articles

Turn It Off! Genetic Switch System Suggests Targeting of Mutant JAK2 Reverses Myeloproliferative Neoplasms

Turn It Off! Genetic Switch System Suggests Targeting of Mutant JAK2 Reverses Myeloproliferative Neoplasms

Near-Infrared Fluorescence Imaging of miRNA Using a Transmembrane Polypeptide-Based Genetic Reporter.

MicroRNAs (miRNAs) are small noncoding RNAs that play important regulatory roles in multiple biological processes. Many miRNAs exhibit unique expression patterns and are considered as theranostic biomarkers in a variety of human diseases. A reporter system that is capable of imaging miRNA in vivo is crucial for investigating miRNA biology. In the present study, an organic anion-transporting polypeptide 1B3 (OATP1B3)-based genetic switch system is designed and optimized to achieve near-infrared fluorescent imaging of miRNA by the uptake of indocyanine green (ICG) dye. The reporter system, named miR-ON-OB3, is shown to be efficient to regulate the expression of OATP1B3 in mammalian cells. Notably, the results indicate that the system is of high sensitivity for near-infrared fluorescence imaging of both exogenous and endogenous miRNA in mammalian cells. Moreover, the system is proved to be functional for real-time near-infrared fluorescence imaging of miRNA in living mice. This study establishes a novel genetic encoded reporter for near-infrared fluorescence imaging of miRNA, which may provide a potential tool for in vivo imaging of miRNA in clinical applications due to the clinical availability of ICG.

Role of Plant Somatic Embryogenesis Receptor Kinases (SERKs) in Cell-to-Embryo Transitional Activity: Key at Novel Assorted Structural Subunits

Somatic Embryogenesis Receptor Kinase (SERK) family of receptor kinases is functionally diverse, involved in cell-to-embryo transition and controlling a number of other fundamental aspects of plant development. The morphological transformation of somatic to embryonic cells has drawn scientific attention utmost due to remarkable genetic-switch system evolved across species. Receptor kinases having direct role in somatic embryogenesis (SE) and involved in other functions are designated as “SERK” and “SERK-like” genes, respectively. We aim for phylogenetic reconstruction to reveal major SERK groups across plant species (angiosperm to gymnosperm) for their functional diversification. Data indicate that the development of SERK proteins occurred prior to the divergence of monocots and eudicots. Also, the SERK orthology is not directly proportional to their functions. Structure prediction results identified novel transmembrane topologies, short linear motifs and O-glycosylation sites exclusively in SERK proteins than SERK-like proteins. Comparative temporal expression analyses of SERK and SERK-like genes provided significant accordance with their physiological function. The identification of intrinsic disordered regions (IDRs) exclusively in SERK proteins was assumed to perceive external stress-induced signals that may lead to rapid protein folding. In a result it switches-on the precise cellular signals essential for the acquisition of SE. Moreover, the regulatory sequences of SERK genes are evolved with unique cellular fate deciding AP2-like ethylene responsive transcription factor AINTEGUMENTA binding sites for their spatial expression in SE. Based on these analyses we suggest future avenues of research that may be imperative for elucidating the importance of SERK gene evolution in SE.

Hybrid Petri net based modeling for biological pathway simulation

Hybrid Petri net (HPN) is an extension of the Petri net formalism, which enables us to handle continuous information in addition to discrete information. Firstly, this paper demonstrates how biological pathways can be modeled by the integration of discrete and continuous elements, with an example of the ? phage genetic switch system including induction and retroregulation mechanisms. Although HPN allows intuitive modeling of biological pathways, some fundamental biological processes such as complex formation cannot be represented with HPN. Thus, this paper next provides the formal definition of hybrid functional Petri net with extension (HFPNe), which has high potential for modeling various kinds of biological processes. Cell Illustrator is a software tool developed on the basis of the definition of HFPNe. Hypothesis creation by Cell Illustrator is demonstrated with the example of the cyanobacterial circadian gene clock system. Finally, our ongoing tasks, which include the development of a computational platform for systems biology, are presented.

Analysis of Genetic Toggle Switch Systems Encoded on Plasmids

Genetic switch systems with mutual repression of two transcription factors, encoded on plasmids, are studied using stochastic methods. The plasmid copy number is found to strongly affect the behavior of these systems. More specifically, the average time between spontaneous switching events quickly increases with the number of plasmids. It was shown before that for a single copy encoded on the chromosome, the exclusive switch is more stable than the general switch. Here we show that when the switch is encoded on a sufficiently large number of plasmids, the situation is reversed and the general switch is more stable than the exclusive switch. These predictions can be tested experimentally using methods of synthetic biology.

Stochastic simulations of genetic switch systems

Genetic switch systems with mutual repression of two transcription factors are studied using deterministic methods (rate equations) and stochastic methods (the master equation and Monte Carlo simulations). These systems exhibit bistability, namely two stable states such that spontaneous transitions between them are rare. Induced transitions may take place as a result of an external stimulus. We study several variants of the genetic switch and examine the effects of cooperative binding, exclusive binding, protein-protein interactions, and degradation of bound repressors. We identify the range of parameters in which bistability takes place, enabling the system to function as a switch. Numerous studies have concluded that cooperative binding is a necessary condition for the emergence of bistability in these systems. We show that a suitable combination of network structure and stochastic effects gives rise to bistability even without cooperative binding. The average time between spontaneous transitions is evaluated as a function of the biological parameters.

Genetic Toggle Switch without Cooperative Binding

Genetic switch systems with mutual repression of two transcription factors are studied using deterministic and stochastic methods. Numerous studies have concluded that cooperative binding is a necessary condition for the emergence of bistability in these systems. Here we show that, for a range of biologically relevant conditions, a suitable combination of network structure and stochastic effects gives rise to bistability even without cooperative binding.

Similar genetic switch systems might integrate the floral inductive pathways in dicots and monocots

A recent paper by Million Tadege et al. shows that a SOC1-like gene from rice, OsSOC1, can complement the Arabidopsis soc1 mutant, and that ectopic expression of the Arabidopsis floral repressor FLC in rice delays flowering and up-regulation of OsSOC1. These findings, together with the identification of the wheat vernalization VRN1 locus as an AP1 homologue, suggest that related genetic switch systems control floral transition in dicots and monocots but that they are based on different MADS-box transcription factors.

Induction of vascular networks in adult organs: implications to proangiogenic therapy.

Most therapeutic proangiogenic approaches rely on the premise that a single factor (e.g., VEGF) can induce new vascular loops properly connected to the existing vasculature of an ill-perfused organ (e.g., the ischemic myocardium). To gain insights into VEGF-driven neovascularization in the adult, in general, and to uncover inherent obstacles in VEGF-based therapeutic angiogenesis, we have used a transgenic system for conditional "on" and "off" switching of VEGF expression in selected adult organs and analytical methods for three-dimensional visualization of the induced vascular network. VEGF induces massive accumulation of endothelial progenitor cells and their subsequent coalescence into new vascular loops. Continual ramification of the vasculature and fusion of adjacent vessels culminate in formation of hemangioma-like vessels. In the absence of guiding cues, abnormal branching patterns and random connections with the existing network are formed. Following cessation of the VEGF stimulus, the acquired network undergoes extensive hemodynamic remodeling acting to "normalize" its architecture. Premature withdrawal of VEGF leads to regression of most acquired vessels, thus challenging the utility of therapeutic approaches relying on short stimulus duration. Overproduction of VEGF leads also to highly disruptive edema, thereby emphasizing the need to uncouple VEGF-induced permeability from its angiogenic activity. This genetic switch system thus highlights remaining problems critical for the implementation of proangiogenic therapy.

A regulatory network for the efficient control of transgene expression.

Expression of heterologous genes in mammalian cells or organisms for therapeutic or experimental purposes often requires tight control of transgene expression. Specifically, the following criteria should be met: no background gene activity in the off-state, high gene expression in the on-state, regulated expression over an extended period, and multiple switching between on- and off-states. Here, we describe a genetic switch system for controlled transgene transcription using chimeric repressor and activator proteins functioning in a novel regulatory network. In the off-state, the target transgene is actively silenced by a chimeric protein consisting of multimerized eukaryotic transcriptional repression domains fused to the DNA-binding tetracycline repressor. In the on-state, the inducer drug doxycycline affects both the derepression of the target gene promoter and activation by the GAL4-VP16 transactivator, which in turn is under the control of an autoregulatory feedback loop. The hallmark of this new system is the efficient transgene silencing in the off-state, as demonstrated by the tightly controlled expression of the highly cytotoxic diphtheria toxin A gene. Addition of the inducer drug allows robust activation of transgene expression. In stably transfected cells, this control is still observed after months of repeated cycling between the repressed and activated states of the target genes. This system permits tight long-term regulation when stably introduced into cell lines. The underlying principles of this network system should have general applications in biotechnology and gene therapy.

The malignant transformation as a metabolic steady state transition: The possible significance of the phasing of enzyme synthesis and related aspects

It has been suggested by Sel'kov and by the author that the malignant transformation may be due to a transition between alternative steady states at the metabolic level without necessarily involving a genetic defect. It had previously been indicated by the author that the properties of a cell can be expected to reflect its pattern of temporal organisation. These two aspects are now considered in relation to one another by examining the behaviour of a coupled enzymic system (involving substrate inhibition characteristics) which is capable of exhibiting multiple steady states. It is shown that the phasing of the synthesis of the enzymes concerned during the cell cycle (normal or disturbed as a result of the action of agents) can determine whether a transition occurs or not and also if it is stable or not. It is also pointed out that the phasing between the fluctuations in the levels of inhibitors and activators of the enzymes involved and in their isozyme patterns can be equally significant in these respects. Hence a transition can be effected by a variety of agents acting at diverse sites within or without the cell. The transition is discussed as an example of a process that may be involved in the malignant transformation. It is emphasized that once a transition has occurred in a cell, there is no reason to presuppose that the new state cannot be inherited by the progeny of that cell, despite the removal of the causative agent: reversal is possible, however, and is discussed as an explanation for abortive oncogenic transformation. Other aspects briefly discussed in relation to metabolic steady state transitions include - the random nature and distribution of transformation in culture; the heterogeneity of transformed cells; resistance to transformation; the significance of the timing and duration of action of an oncogenic agent; the effect of gene duplication on the ‘fixation’ of the transformation; cell death. Finally it is pointed out that the same considerations are likely to apply to other systems exhibiting multiple steady states as a result of the existence of the phenomenon of hysteresis and hence probably to genetic switch systems also.